RNAsoft - Software for RNA/DNA secondary structure prediction and design

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AveRNA combines the RNA secondary structures predicted by different algorithms to increase the overall accuracy
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PairFold predicts the minimum free energy secondary structure formed by two input DNA or RNA molecules. PairFold can be used, for example, to predict interactions between a probe and target RNA molecule, or between pairs of strands in biomolecular nanostructures.
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[ About ]
CombFold predicts which strand, out of a combinatorial set formed from DNA or RNA input strands, folds to a secondary structure with the lowest minimum free energy. CombFold can, for example, efficiently test that no strand in a large tag library forms unwanted secondary structure.
RNA Designer
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RNA Designer designs an RNA sequence that folds to a given input secondary structure. The tool is intended for designers of RNA molecules with particular structural or functional properties.
HotKnots 2.0
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HotKnots predicts RNA secondary structures with pseudoknots. The tool is intended for use of short RNA sequences that are expected to form pseudoknots.